Comparative study of RNA-Seq and Microarray-derived coexpression networks

Coexpression networks are data-derived representations of genes behaving in a similar way across tissues and experimental conditions. They have been used for hypothesis generation and guilt-by-association approaches for inferring functions of previously unknown genes. So far, the main platform for expression data has been DNA microarrays, however the recent development of RNA-seq allows for higher accuracy and coverage of transcript populations. It is therefore important to assess the potential for biological investigation of coexpression networks derived from this novel technique in a condition-independent dataset.

A team led by researchers at Institute of Applied Genomics Italy collected 65 publicly available Illumina RNA-seq high quality Arabidopsis thaliana samples and generated Pearson correlation coexpression networks. These networks were then compared with those derived from analogous microarray data. They show how Variance-Stabilizing-Transformed (VST) RNA-seq data samples are the most similar to microarray ones, with respect to inter-sample variation, correlation coefficient distribution and network topological architecture. Microarray networks show a slightly higher score in biology-derived quality assessments such as overlap with the known protein-protein interaction network and edge ontological agreement.

Different coexpression network centralities are investigated; in particular, they show how betweenness centrality is generally a positive marker for essential genes in Arabidopsis thaliana, regardless of the platform originating the data. In the end, the team focused on a specific gene network case, showing that, although microarray data seem more suited for gene network reverse engineering, RNA-seq offers the great advantage of extending coexpression analyses to the entire transcriptome.

  • Giorgi FM, Del Fabbro C, Licausi F. (2013) Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana. Bioinformatics [Epub ahead of print]. [abstract]